第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* Hydrogen molecule [#ga16bb23]
In this tutorial, how to execute pw.x and how to converge...
How to optimize the molecular geometry is also described.~
In a standard plane-wave pseudopotential code, three-dime...
In this case, the accuracy of the calculation is controll...
#Contents
** Preliminary [#ua6b3fe2]
** SCF calculation [#wcd8fa25]
Let us begin with an SCF calculation of H2 having the exp...
&control
calculation = 'scf'
restart_mode = 'from_scratch',
pseudo_dir = '/home/ikutaro/QE/pseudo/'
outdir = './tmp/'
prefix = 'h2'
tprnfor = .true.
forc_conv_thr = 1.d-4
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd = 4
ecutwfc = 30.0
ecutrho = 120.0
/
&electrons
diagonalization = 'david'
conv_thr = 1.0e-12
mixing_beta = 0.1
/
ATOMIC_SPECIES
H 0.0000 H_ONCV_PBE-1.0.upf
ATOMIC_POSITIONS (angstrom)
H 0.000000000000 0.000000000000 0.0000000...
H 0.000000000000 0.000000000000 0.7400000...
K_POINTS (gamma)
Here the number of electron is 2 and thus the minimum num...
Note "pseudo_dir" and "outdir" should be modified accordi...
To perform the SCF calculation, we use pw.x.
Here let us assume we are going to use pw.x in $HOME/QE/s...
$ mpirun -np 2 $HOME/QE/src/qe-6.6/bin/pw.x < h2_scf.in ...
or for the group's cluster execute
$ qsub h2.sh
where the job script "h2.sh" looks like
#$ -S /bin/bash
#$ -cwd
#$ -q xe1.q
#$ -pe x8 8
#$ -N H2
#
module load intel/2020.2.254
module load intelmpi/2020.2.254
#
INPUT_FILE='h2_scf.in'
OUTPUT_FILE='h2_scf.out'
#
PW_DIR=/home/ikutaro/QE/src/qe-6.6/bin
#
MPI_COMMAND=mpirun
PW_COMMAND=pw.x
PW=$PW_DIR/$PW_COMMAND
#
I_MPI_PIN=1
I_MPI_FABRICS=shm:ofa
OMP_NUM_THREADS=1
#
cat $PE_HOSTFILE | awk '{ print $1":"$2/ENVIRON["OMP_NUM...
hostfile.$JOB_ID
#
$MPI_COMMAND $PW < $INPUT_FILE > $OUTPUT_FILE
When the calculation starts, you can see the following he...
Program PWSCF v.6.6 starts on 20Jan2021 at 10:38:59
This program is part of the open-source Quantum ESP...
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter ...
"P. Giannozzi et al., J. Phys.:Condens. Matter ...
URL http://www.quantum-espresso.org",
in publications or presentations arising from this ...
http://www.quantum-espresso.org/quote
When the SCF convergence is archived, the following can b...
! total energy = -2.31431570 Ry
estimated scf accuracy < 5.3E-13 Ry
The total energy is the sum of the following terms:
one-electron contribution = -3.79278260 Ry
hartree contribution = 2.01958267 Ry
xc contribution = -1.37197485 Ry
ewald contribution = 0.83085908 Ry
convergence has been achieved in 15 iterations
If "tprnfor = .true." the following lines can also be found
Forces acting on atoms (cartesian axes, Ry/au):
atom 1 type 1 force = 0.00000000 0.000...
atom 2 type 1 force = 0.00000000 0.000...
Total force = 0.042606 Total SCF correction...
Use the "less" or "more" command to see the file.
** Convergence study [#g0f7b800]
*** Convergence wrt cutoff [#b2656295]
To study the convergence of the total energy, we calculat...
Results are as follows
# ecutwfc (Ry) total energy (Ry)
30.0 -2.31431279
40.0 -2.32593152
50.0 -2.33045981
60.0 -2.33201780
70.0 -2.33257560
80.0 -2.33275476
90.0 -2.33280832
100.0 -2.33281717
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
*** Convergence wrt box size [#b3914639]
Then let us calculate the total energy as a function of t...
# a (Angstrom) total energy (Ry)
5.0 -2.33788501
10.0 -2.33201780
15.0 -2.33202479
20.0 -2.33202183
25.0 -2.33202063
30.0 -2.33202053
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
** Optimizing the bond length (1) [#cd8a50a0]
Let us determine the bond length of H2. First, we calcula...
1.30 -2.32657183
1.32 -2.32840377
1.34 -2.32984183
1.36 -2.33091143
1.38 -2.33163627
1.40 -2.33203866
1.42 -2.33213950
1.44 -2.33195843
1.46 -2.33151384
1.48 -2.33082299
1.50 -2.32990212
By fitting the total energy to 6th-order polynomial, the ...
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
** Optimizing the bond length (2) [#tad1e55c]
Alternatively, one can optimize the geometry (internal co...
&control
calculation = 'relax'
restart_mode = 'from_scratch',
pseudo_dir = '/home/ikutaro/QE/pseudo/'
outdir = './tmp/'
prefix = 'h2'
tprnfor = .true.
forc_conv_thr = 1.d-4
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd = 4
ecutwfc = 30.0
ecutrho = 120.0
/
&electrons
diagonalization = 'david'
conv_thr = 1.0e-12
mixing_beta = 0.1
/
&ions
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
H 0.0000 H_ONCV_PBE-1.0.upf
ATOMIC_POSITIONS (angstrom)
H 0.000000000000 0.000000000000 0.0000000...
H 0.000000000000 0.000000000000 0.7400000...
K_POINTS (gamma)
The main differences from the SCF calculation are
calculation = 'relax'
and
&ions
ion_dynamics='bfgs'
/
Here we use the BFGS algorithm for the structural optimiz...
Note the namelist &ions should be given even though the d...
In such a case
&ions
/
can be used. When the convergence for the structural rela...
bfgs converged in 4 scf cycles and 3 bfgs steps
(criteria: energy < 1.0E-04 Ry, force < 1.0E-04 R...
End of BFGS Geometry Optimization
and the final coordinates follow as:
Begin final coordinates
ATOMIC_POSITIONS (angstrom)
H 0.0000000000 0.0000000000 -0....
H 0.0000000000 0.0000000000 0....
End final coordinates
The bond length of 1.4169 Bohr (0.750 Angstrom) obtained ...
*** Exercise [#r4176331]
The bond length also depends on the computational paramet...
終了行:
* Hydrogen molecule [#ga16bb23]
In this tutorial, how to execute pw.x and how to converge...
How to optimize the molecular geometry is also described.~
In a standard plane-wave pseudopotential code, three-dime...
In this case, the accuracy of the calculation is controll...
#Contents
** Preliminary [#ua6b3fe2]
** SCF calculation [#wcd8fa25]
Let us begin with an SCF calculation of H2 having the exp...
&control
calculation = 'scf'
restart_mode = 'from_scratch',
pseudo_dir = '/home/ikutaro/QE/pseudo/'
outdir = './tmp/'
prefix = 'h2'
tprnfor = .true.
forc_conv_thr = 1.d-4
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd = 4
ecutwfc = 30.0
ecutrho = 120.0
/
&electrons
diagonalization = 'david'
conv_thr = 1.0e-12
mixing_beta = 0.1
/
ATOMIC_SPECIES
H 0.0000 H_ONCV_PBE-1.0.upf
ATOMIC_POSITIONS (angstrom)
H 0.000000000000 0.000000000000 0.0000000...
H 0.000000000000 0.000000000000 0.7400000...
K_POINTS (gamma)
Here the number of electron is 2 and thus the minimum num...
Note "pseudo_dir" and "outdir" should be modified accordi...
To perform the SCF calculation, we use pw.x.
Here let us assume we are going to use pw.x in $HOME/QE/s...
$ mpirun -np 2 $HOME/QE/src/qe-6.6/bin/pw.x < h2_scf.in ...
or for the group's cluster execute
$ qsub h2.sh
where the job script "h2.sh" looks like
#$ -S /bin/bash
#$ -cwd
#$ -q xe1.q
#$ -pe x8 8
#$ -N H2
#
module load intel/2020.2.254
module load intelmpi/2020.2.254
#
INPUT_FILE='h2_scf.in'
OUTPUT_FILE='h2_scf.out'
#
PW_DIR=/home/ikutaro/QE/src/qe-6.6/bin
#
MPI_COMMAND=mpirun
PW_COMMAND=pw.x
PW=$PW_DIR/$PW_COMMAND
#
I_MPI_PIN=1
I_MPI_FABRICS=shm:ofa
OMP_NUM_THREADS=1
#
cat $PE_HOSTFILE | awk '{ print $1":"$2/ENVIRON["OMP_NUM...
hostfile.$JOB_ID
#
$MPI_COMMAND $PW < $INPUT_FILE > $OUTPUT_FILE
When the calculation starts, you can see the following he...
Program PWSCF v.6.6 starts on 20Jan2021 at 10:38:59
This program is part of the open-source Quantum ESP...
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter ...
"P. Giannozzi et al., J. Phys.:Condens. Matter ...
URL http://www.quantum-espresso.org",
in publications or presentations arising from this ...
http://www.quantum-espresso.org/quote
When the SCF convergence is archived, the following can b...
! total energy = -2.31431570 Ry
estimated scf accuracy < 5.3E-13 Ry
The total energy is the sum of the following terms:
one-electron contribution = -3.79278260 Ry
hartree contribution = 2.01958267 Ry
xc contribution = -1.37197485 Ry
ewald contribution = 0.83085908 Ry
convergence has been achieved in 15 iterations
If "tprnfor = .true." the following lines can also be found
Forces acting on atoms (cartesian axes, Ry/au):
atom 1 type 1 force = 0.00000000 0.000...
atom 2 type 1 force = 0.00000000 0.000...
Total force = 0.042606 Total SCF correction...
Use the "less" or "more" command to see the file.
** Convergence study [#g0f7b800]
*** Convergence wrt cutoff [#b2656295]
To study the convergence of the total energy, we calculat...
Results are as follows
# ecutwfc (Ry) total energy (Ry)
30.0 -2.31431279
40.0 -2.32593152
50.0 -2.33045981
60.0 -2.33201780
70.0 -2.33257560
80.0 -2.33275476
90.0 -2.33280832
100.0 -2.33281717
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
*** Convergence wrt box size [#b3914639]
Then let us calculate the total energy as a function of t...
# a (Angstrom) total energy (Ry)
5.0 -2.33788501
10.0 -2.33201780
15.0 -2.33202479
20.0 -2.33202183
25.0 -2.33202063
30.0 -2.33202053
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
** Optimizing the bond length (1) [#cd8a50a0]
Let us determine the bond length of H2. First, we calcula...
1.30 -2.32657183
1.32 -2.32840377
1.34 -2.32984183
1.36 -2.33091143
1.38 -2.33163627
1.40 -2.33203866
1.42 -2.33213950
1.44 -2.33195843
1.46 -2.33151384
1.48 -2.33082299
1.50 -2.32990212
By fitting the total energy to 6th-order polynomial, the ...
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
** Optimizing the bond length (2) [#tad1e55c]
Alternatively, one can optimize the geometry (internal co...
&control
calculation = 'relax'
restart_mode = 'from_scratch',
pseudo_dir = '/home/ikutaro/QE/pseudo/'
outdir = './tmp/'
prefix = 'h2'
tprnfor = .true.
forc_conv_thr = 1.d-4
/
&system
ibrav = 1
A = 10.d0
nat = 2
ntyp = 1
nbnd = 4
ecutwfc = 30.0
ecutrho = 120.0
/
&electrons
diagonalization = 'david'
conv_thr = 1.0e-12
mixing_beta = 0.1
/
&ions
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
H 0.0000 H_ONCV_PBE-1.0.upf
ATOMIC_POSITIONS (angstrom)
H 0.000000000000 0.000000000000 0.0000000...
H 0.000000000000 0.000000000000 0.7400000...
K_POINTS (gamma)
The main differences from the SCF calculation are
calculation = 'relax'
and
&ions
ion_dynamics='bfgs'
/
Here we use the BFGS algorithm for the structural optimiz...
Note the namelist &ions should be given even though the d...
In such a case
&ions
/
can be used. When the convergence for the structural rela...
bfgs converged in 4 scf cycles and 3 bfgs steps
(criteria: energy < 1.0E-04 Ry, force < 1.0E-04 R...
End of BFGS Geometry Optimization
and the final coordinates follow as:
Begin final coordinates
ATOMIC_POSITIONS (angstrom)
H 0.0000000000 0.0000000000 -0....
H 0.0000000000 0.0000000000 0....
End final coordinates
The bond length of 1.4169 Bohr (0.750 Angstrom) obtained ...
*** Exercise [#r4176331]
The bond length also depends on the computational paramet...
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